Insights into the Substrate Specificity of a Thioesterase Rv0098 of Mycobacterium Tuberculosis through X-ray Crystallographic and Molecular Dynamics Studies

The crystal structure of Rv0098, a long-chain fatty acyl-CoA thioesterase from Mycobacterium tuberculosis with bound dodecanoic acid at the active site provided insights into the mode of substrate binding but did not reveal the structural basis of substrate specificities of varying chain length. Molecular dynamics studies demonstrated that certain residues of the substrate binding tunnel are flexible and thus modulate the length of the tunnel. The flexibility of the loop at the base of the tunnel was also found to be important for determining the length of the tunnel for accommodating appropriate substrates. A combination of crystallographic and molecular dynamics studies thus explained the structural basis of accommodating long chain substrates by Rv0098 of M. tuberculosis.

On an Integrated Transfer Matrix method for multiply connected mufflers

The commercial automotive mufflers are generally of a complicated shape with multiply connected parts and complex acoustic elements. The analysis of such complex mufflers has always been a great challenge. In this paper, an Integrated Transfer Matrix method has been developed to analyze complex mufflers. Integrated transfer matrix relates the state variables across the entire cross-section of the muffler shell, as one moves along the axis of the muffler, and can be partitioned appropriately in order to relate the state variables of different tubes constituting the cross-section. The paper presents a generalized one-dimensional (1-D) approach, using the transfer matrices of simple acoustic elements, which are available from the literature. The present approach is robust and flexible owing to its capability to construct an overall matrix of the muffler with the transfer matrices of individual acoustic elements and boundary conditions, which can then be used to evaluate the transmission loss, insertion loss, etc. Results from the present approach have been validated through comparisons with the available experimental and three-dimensional finite element method (FEM) based results. The results show good agreement with both measurements and FEM analysis up to the cut-off frequency. (C) 2011 Elsevier Ltd. All rights reserved.

Carbon nanotube mat as substrate for ZnO nanotip field emitters

We have reported the synthesis of ZnO nanotips on a multi walled carbon nanotube (MWCNT) mat by a vapour transport process. This combination of ZnO nanotips and a MWCNT mat exhibit ideal field emission behaviour. The turn on field and threshold field is found to be 0.34 and 1.5 V mu m(-1), respectively. The low threshold field is due to the good adherence of the ZnO nanotips on the MWCNT mat. The field enhancement factor is found to be 5 x 10(2) which is in agreement with the intrinsic field emission factor of ZnO nanotips. The emission current is found to be highly stable even at moderate vacuum.

The substrate dependent competitive formation of cyclobutanones and cyclopentanones in an intramolecular rhodium carbenoid CH insertion reaction: enantiospecific total synthesis of silphiperfol-6-ene

The enantiospecific total synthesis of silphiperfol-6-ene has been accomplished starting from the readily available monoterpene (R)-limonene, employing a rhodium carbenoid insertion into the CH bond of a tertiary methyl group. A substrate dependent competitive insertion of the rhodium carbenoid in the gamma- and beta-CH bonds to form cyclopentanone and cyclobutanones, respectively, has been described. (C) 2012 Elsevier Ltd. All rights reserved.

Self Repair in Circuits-Automating Open Fault Repair in Integrated Circuits Using Field-Induced Aggregation of Carbon Nanotubes

This paper presents studies on the use of carbon nanotubes dispersed in an insulating fluid to serve as an automaton for healing open-circuit interconnect faults in integrated circuits. The physics behind the repair mechanism is the electric-field-induced diffusion limited aggregation. On the occurrence of an open fault, the repair is automatically triggered due to the presence of an electric field across the gap. We perform studies on the repair time as a function of the electric field and dispersion concentrations with the above application in mind.

Structural and Mutational Studies on Substrate Specificity and Catalysis of Salmonella typhimurium D-Cysteine Desulfhydrase

Salmonella typhimurium DCyD (StDCyD) is a fold type II pyridoxal 5' phosphate (PLP)-dependent enzyme that catalyzes the degradation of D-Cys to H2S and pyruvate. It also efficiently degrades beta-chloro-D-alanine (beta CDA). D-Ser is a poor substrate while the enzyme is inactive with respect to L-Ser and 1-amino-1-carboxy cyclopropane (ACC). Here, we report the X-ray crystal structures of StDCyD and of crystals obtained in the presence of D-Cys, beta CDA, ACC, D-Ser, L-Ser, D-cycloserine (DCS) and L-cycloserine (LCS) at resolutions ranging from 1.7 to 2.6 angstrom. The polypeptide fold of StDCyD consisting of a small domain (residues 48-161) and a large domain (residues 1-47 and 162-328) resembles other fold type II PLP dependent enzymes. The structures obtained in the presence of D-Cys and beta CDA show the product, pyruvate, bound at a site 4.0-6.0 angstrom away from the active site. ACC forms an external aldimine complex while D- and L-Ser bind non-covalently suggesting that the reaction with these ligands is arrested at C alpha proton abstraction and transimination steps, respectively. In the active site of StDCyD cocrystallized with DCS or LCS, electron density for a pyridoxamine phosphate (PMP) was observed. Crystals soaked in cocktail containing these ligands show density for PLP-cycloserine. Spectroscopic observations also suggest formation of PMP by the hydrolysis of cycloserines. Mutational studies suggest that Ser78 and Gln77 are key determinants of enzyme specificity and the phenolate of Tyr287 is responsible for C alpha proton abstraction from D-Cys. Based on these studies, a probable mechanism for the degradation of D-Cys by StDCyD is proposed.

INST: An Integrated Steering Framework for Critical Weather Applications

Online remote visualization and steering of critical weather applications like cyclone tracking are essential for effective and timely analysis by geographically distributed climate science community. A steering framework for controlling the high-performance simulations of critical weather events needs to take into account both the steering inputs of the scientists and the criticality needs of the application including minimum progress rate of simulations and continuous visualization of significant events. In this work, we have developed an integrated user-driven and automated steering framework INST for simulations, online remote visualization, and analysis for critical weather applications. INST provides the user control over various application parameters including region of interest, resolution of simulation, and frequency of data for visualization. Unlike existing efforts, our framework considers both the steering inputs and the criticality of the application, namely, the minimum progress rate needed for the application, and various resource constraints including storage space and network bandwidth to decide the best possible parameter values for simulations and visualization.

Radiative and non-radiative effects of a substrate on localized plasmon resonance of particles

Experiments have shown strong effects of some substrates on the localized plasmons of metallic nano particles but they are inconclusive on the affecting parameters. Here, we have used discrete dipole approximation in conjunction with Sommerfeld integral relations to explain the effect of the substrates as a function of the parameters of incident radiation. The radiative coupling can both quench and enhance the resonance and its dependence on the angle and polarization of incident radiation with respect to the surface is shown. Non-radiative interaction with the substrate enhances the plasmon resonance of the particles and can shift the resonances from their free-space energies significantly. The non-radiative interaction of the substrate is sensitive to the shape of particles and polarization of incident radiation with respect to substrate. Our results show that the plasmon resonances in coupled and single particles can be significantly altered from their free-space resonances and are quenched or enhanced by the choice of substrate and polarization of incident radiation. (C) 2012 American Institute of Physics. http://dx.doi.org/10.1063/1.4736544]

Substrate temperature influenced physical properties of silicon MOS devices with TiO2 gate dielectric

DC reactive magnetron sputtering technique was employed for deposition of titanium dioxide (TiO2) films. The films were formed on Corning glass and p-Si (100) substrates by sputtering of titanium target in an oxygen partial pressure of 6x10-2 Pa and at different substrate temperatures in the range 303 673 K. The films formed at 303 K were X-ray amorphous whereas those deposited at substrate temperatures?=?473 K were transformed into polycrystalline nature with anatase phase of TiO2. Fourier transform infrared spectroscopic studies confirmed the presence of characteristic bonding configuration of TiO2. The surface morphology of the films was significantly influenced by the substrate temperature. MOS capacitor with Al/TiO2/p-Si sandwich structure was fabricated and performed currentvoltage and capacitancevoltage characteristics. At an applied gate voltage of 1.5 V, the leakage current density of the device decreased from 1.8?x?10-6 to 5.4?x?10-8 A/cm2 with the increase of substrate temperature from 303 to 673 K. The electrical conduction in the MOS structure was more predominant with Schottky emission and Fowler-Nordheim conduction. The dielectric constant (at 1 MHz) of the films increased from 6 to 20 with increase of substrate temperature. The optical band gap of the films increased from 3.50 to 3.56 eV and refractive index from 2.20 to 2.37 with the increase of substrate temperature from 303 to 673 K. Copyright (c) 2012 John Wiley & Sons, Ltd.

Enhanced Raman Spectroscopy of Molecules Adsorbed on Carbon-Doped TiO2 Obtained from Titanium Carbide: A Visible-Light-Assisted Renewable Substrate

Titanium carbide (TiC) is an electrically conducting material with favorable electrochemical properties. In the present studies, carbon-doped TiO2 (C-TiO2) has been synthesized from TiC particles, as well as TiC films coated on stainless steel substrate via thermal annealing under various conditions. Several C-TiO2 substrates are synthesized by varying experimental, conditions and characterized by UV-visible spectroscopy, photoluminescence, X-ray diffraction and X-ray photoelectron spectroscopic techniques. C-TiO2 in the dry state (in powder form as well as in film form) is subsequently used as a substrate for enhancing Raman signals corresponding to 4-mercaptobenzoic acid and 4-nitrothiophenol by utilizing chemical enhancement based on charge-transfer interactions. Carbon, a nonmetal dopant in TiO2, improves the intensities of Raman signals, compared, to undoped TiO2. Significant dependence of Raman intensity on carbon doping is observed. Ameliorated performance obtained using C-TiO2 is attributed to the presence of surface defects that originate due to carbon as a dopant, which, in turn,, triggers charge transfer between TiO2 and analyte. The C-TiO2 substrates are subsequently regenerated for repetitive use by illuminating an analyte-adsorbed substrate with visible light for a period of 5 h.

Effect of Interfacial Microstructure of Adsorbed Poly(ethylene glycol) Monooleate on Steel Substrate on Sliding Friction in Oil in Water Emulsion

The concentration of a nonionic surfactant and water pH were varied in an oil-in-water emulsion to minimize the friction coefficient between a steel ball sliding on a steel flat. At a surfactant concentration near the CMC (critical micelle concentration) the oil droplet size was found to be minimum. In this paper we study the microstructure of the surfactant molecules self-assembled on the steel substrate in water to comment on the ability of the surfactant aggregate to attract and retain oil. We find that a near semicylindrical hemimiceller microstructure with hydrocarbon tails projecting into bulk water as obtained at CMC in near neutral water is best able to capture and retain oil in yielding a low coefficient of friction.

Integrated parallelization of computations and visualization for large-scale applications

Critical applications like cyclone tracking and earthquake modeling require simultaneous high-performance simulations and online visualization for timely analysis. Faster simulations and simultaneous visualization enable scientists provide real-time guidance to decision makers. In this work, we have developed an integrated user-driven and automated steering framework that simultaneously performs numerical simulations and efficient online remote visualization of critical weather applications in resource-constrained environments. It considers application dynamics like the criticality of the application and resource dynamics like the storage space, network bandwidth and available number of processors to adapt various application and resource parameters like simulation resolution, simulation rate and the frequency of visualization. We formulate the problem of finding an optimal set of simulation parameters as a linear programming problem. This leads to 30% higher simulation rate and 25-50% lesser storage consumption than a naive greedy approach. The framework also provides the user control over various application parameters like region of interest and simulation resolution. We have also devised an adaptive algorithm to reduce the lag between the simulation and visualization times. Using experiments with different network bandwidths, we find that our adaptive algorithm is able to reduce lag as well as visualize the most representative frames.